Seeing as I have the same problem, from time to time, I'll chime in.
What I've learned about me is that I'm not consistent from day to day especially when shooting from different spots. It takes me a while to get consistent from each shooting spot. By spot I mean "hide" where I groom the ground over a period of time to get it where I like it for prone shooting long distances.
From time to time I have the same problem from my home prone 300 yard range when I check zeros. If the first cold bore zero shot @ 300 is off it's always because of me.
This becomes worse when I switch from my lesser 270 AM to the more robust 375 AM. Any body position is greatly magnified.
Recent experience:
Set up to check zero after not having shot the big girl for several months.
POI was 1.25 MOA low. 2-shot group was 1.5" vertical, 0 horizontal. She does better than that. A couple of adjustments and shots and she was zero'd. But after the couple of adjustments I was back where I started. I've done this many times during my life.
Months earlier I easily spotted all shots from 300 to 1K.
For these shots she was jumping violently to the left with not a chance of spotting the shot.
The following video proves that it isn't the rifle that is the problem.
Once I got consistent with my shooting position, after watching the video, things settled in pretty well.
What I am suggesting is that consistency is the key.
[URL=http://i12.photobucket.com/albums/a243/royinidaho/MVI_2771_zps17dd74a7.mp4][/URL]